Virgin’s flight VA 469 was due to arrive in Brisbane at 8.10pm on Friday.
Instead, the flight was delayed for take-off in Perth and arrived at 1.20am on Saturday morning.
Virgin said the delay was due to an engineering matter.
While passengers were up in the air, Queensland’s health advice was updated to say anyone coming in from Perth or Peel from midnight on Friday night had to enter 14 days quarantine after the WA city entered a snap three-day lockdown.
Passengers came off the plane and were taken directly to buses and shuffled to nearby hotels.
It is understood an exemption has been granted so the passengers don’t have to pay for the unexpected hotel stays.